I am using the latest version on Mediacode iPhone Edition. I just downloaded the version on your website today (07/11/2012). I cannot check the version because of the problem described below:

I put some files to the queue and start coding. I minimize the main window and also minimize the small window with the video preview. I leave the program like that until the coding finishes.

After this I cannot restore the main window. Even if I close the program using the tray icon and restarted I can only see the tray icon and nothing else. The "Show Interface" on the tray menu does not help either. I had to re-install the app to make the window visible again.